Retroflexion during colonoscopy is typically only practiced in the wider proximal and distal ends of the large intestine owing to the stiff nature of the colonoscope. This inability to examine the proximal side of the majority of colon folds contributes to today’s suboptimal colorectal cancer detection rates. We have developed an algorithm for autonomous retroflexion of a flexible endoscope that is actuated magnetically from the tip. The magnetic wrench applied on the tip of the endoscope is optimized in real-time with data from pose detection to compute motions of the actuating magnet. This is the first example of a completely autonomous maneuver by a magnetic endoscope for exploration of the gastrointestinal tract. The proposed approach was validated in plastic tubes of various diameters with a success rate of 98.8% for separation distances up to 50 mm. Additionally, a set of trials was conducted in an excised porcine colon observing a success rate of 100% with a mean time of 19.7 s. In terms of clinical safety, the maximum stress that is applied on the colon wall with our methodology is an order of magnitude below what would damage tissue.